Translation initiation factor 4E in complex with (rp)-M2(7,2'O)GPPSPG mRNA 5' cap analog (beta-S-arca D1)

Structure

x-ray diffraction · 3 distinct chains · 35% helix, 30% strand (DSSP).

Ligands and binding sites

• WZO · [(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-7-ium-9-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl [phosphonooxy(sulfanyl) phosphoryl] hydrogen phosphate · ligand · 3 copies · chains A, B, C
• GOL · Glycerol · additive · chains B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• B–C · 370 Ų buried · 6 hydrogen bonds · protein-protein
• A–D · 364 Ų buried · 5 hydrogen bonds · protein-protein
• A–B · 343 Ų buried · 2 hydrogen bonds · protein-protein

Compared structures

• 5M7V · Translation initiation factor 4E in complex with (RP)-m2(7,2'O)GppSpG mRNA 5' cap analog… · the same entry in another collection · chain A against A, TM-score 1.00
• P63073 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 4E (P63073) · a predicted model of the same protein · chain A against A, TM-score 0.98

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P63073
• Elsewhere: RCSB PDB 5M7V · PDBe 5M7V · UniProt P63073